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Erik Karlsson

@eakarlsson.bsky.social
2.3K followers 242 following 115 posts

Emerging/endemic infectious diseases, mostly viruses. Pandemic Prevention. Early Warning. One Health. Science outside-the-box. Views my own. 🦠🧪🔬🐓🦇

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Erik Karlsson @eakarlsson.bsky.social · 21/09/2026
#COVID-19 didn’t make avian #influenza disappear. But among #Cambodian #poultry workers, #PPE use, awareness, and training all fell as incomes tightened. The hopeful part? This is fixable: affordable PPE, training, and advice from people workers trust. onlinelibrary.wiley.com/doi/10.1111/...
onlinelibrary.wiley.com
Impact of the COVID‐19 Pandemic on Knowledge, Attitudes, and Practices Related to Avian Influenza Among Poultry Workers in Cambodia
Background Live bird markets (LBMs) are high-risk environments for the amplification and transmission of avian influenza viruses (AIVs). In Cambodia, limited data exist on knowledge, attitudes, and ...
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Erik Karlsson @eakarlsson.bsky.social · 21/09/2026
A wild animal does not become biologically neutral because someone puts a fence around it. Our new review compares #zoonotic risks in farmed vs wild-caught #wildlife sold for food. The inconvenient answer: origin alone is not risk assessment. www.sciencedirect.com/science/arti... #OneHealth
sciencedirect.com
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Erik Karlsson @eakarlsson.bsky.social · 21/09/2026
#Influenza viruses have 8 genome segments. When 2 infect the same host, evolution can shuffle the deck. Our new EID Perspective examines reassortment and #H5N1 spillover in Asia and why surveillance must detect what viruses have become. wwwnc.cdc.gov/eid/article/...
wwwnc.cdc.gov
Reassortment of Highly Pathogenic Avian Influenza as a Driver for Zoonotic Spillover, Asia
Reassortment of HPAI as Driver for Spillover
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Mike Coston @fla-medic.bsky.social · 22/04/2026
AFD Blog `Cambodian MOH Announces 4th Human #H5N1 Case of 2026' h/t @eakarlsson.bsky.social afludiary.blogspot.com/2026/04/camb...
afludiary.blogspot.com
Cambodian MOH Announces 4th Human H5N1 Case of 2026
#19,125 With thanks for the head's up from  @E_A_Karlsson , we have the following announcement from Cambodia's Ministry of Health on their...
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Erik Karlsson @eakarlsson.bsky.social · 22/04/2026
4th human #H5N1 case of 2026 in #Cambodia A 66-year-old woman from Svay Rieng province, currently hospitalized and receiving treatment. 2026: 4 cases, 0 deaths Since 2023: 38 cases, 15 deaths (CFR 39.5%) Since 2004: 94 cases, 52 deaths (CFR 55.3%) 🧪🦠💉🥼🔬😷🐓
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Mike Coston @fla-medic.bsky.social · 31/03/2026
AFD Blog `Cambodian MOH Announces 3rd Human #H5N1 Case of 2026' h/t @eakarlsson.bsky.social afludiary.blogspot.com/2026/03/camb...
afludiary.blogspot.com
Cambodian MOH Announces 3rd Human H5N1 Case of 2026
#19,102 With thanks for the head's up from   @E_A_Karlsson , we have the following announcement from Cambodia's Ministry of Health on thei...
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Erik Karlsson @eakarlsson.bsky.social · 31/03/2026
3rd human #H5N1 case of 2026 in #Cambodia A 3-year-old boy from Oddar Meanchey province, currently hospitalized and receiving treatment. 🔬🧪😷🐓🦠🥼💉 2026: 3 cases, 0 deaths Since 2023: 37 cases, 15 deaths (CFR 40.5%) Since 2004: 93 cases, 52 deaths (CFR 55.9%)
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Erik Karlsson @eakarlsson.bsky.social · 15/03/2026
Cambodia confirms 2nd human #H5N1 case of 2026 in a 45-year-old woman from Banteay Meanchey province. Patient hospitalized and under treatment. 🥼🦠😷🔬🐓🧪💉 2026: 2 cases, 0 deaths Since 2023: 36 cases, 15 deaths (CFR 41.7%) Since 2004: 92 cases, 52 deaths (CFR 56.5%) #AvianInfluenza #BirdFlu
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Erik Karlsson @eakarlsson.bsky.social · 07/03/2026
Applications are now open for the 7th ISRV School of Respiratory Viruses, hosted by the School of Public Health at The University of Hong Kong. Program details: isrv.eventsair.com/7th-isrv-sch... Apply here: isrv.eventsair.com/Presentation... Applications close: 30 April (UTC+8) 🦠🐓🧪😷🥼💉🔬
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Erik Karlsson @eakarlsson.bsky.social · 14/02/2026
First human #H5N1 case of 2026 in #Cambodia: a 30-year-old man from Kampot province. Sequencing, virus isolation & animal investigations ongoing. Dead chicken at home before onset. Patient has since recovered. 🦠💉😷🐓🥼🔬🧪 Sequencing, contact tracing, and poultry investigations ongoing.
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Metagenomic Virus Discovery workshop @virus-metagenomics.bsky.social · 16/01/2026
Planning is underway for the 2026 Metagenomic Virus Discovery workshop. Last years workshop was a great success with 22 participants representing 11 countries. If you would like to know more, get in contact with our organising committee at mvdworkshop2025@gmail.com
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Erik Karlsson @eakarlsson.bsky.social · 14/01/2026
In our recent @nature.com Communications study, we compared traditional #poultry swabs with environmental #metagenomics, sampling #air, cage surfaces, carcass wash water, and drinking water in two Cambodian live bird markets. 🦠😷🔬🧪🐓🥼 www.nature.com/articles/s41...
nature.com
Client Challenge
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Erik Karlsson @eakarlsson.bsky.social · 26/11/2025
The WHO/WOAH/FAO H5 Evolution Working Group just released a major nomenclature update: 12 new H5 clades across 2.3.2.1 and 2.3.4.4, the result of a decade of relentless viral evolution stretching from Asia to Africa, the Americas, and even Antarctica. 🥼🔬🧪🦠🐓😷 www.biorxiv.org/content/10.1...
biorxiv.org
Nomenclature updates to the hemagglutinin gene clade designations resulting from the continued evolution of high pathogenicity avian influenza A(H5) virus clades 2.3.2.1c and 2.3.4.4
The evolutionary divergence of the A(H5) hemagglutinin (HA) gene of high pathogenicity avian influenza (HPAI) viruses (A/goose/Guangdong/96 lineage) was analyzed by phylogenetic and average pairwise d...
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Pretzel @krispyhajkowicz.bsky.social · 19/11/2025
Go @eakarlsson.bsky.social knocking it out of the park at the @virus-metagenomics.bsky.social workshop at CERI in Stellenbosch.
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Metagenomic Virus Discovery workshop @virus-metagenomics.bsky.social · 18/11/2025
Tomorrow evening we have our keynote lecture session from 16:00 in the Neelsie Cinema, Stellenbosch University. Dr Maja Vukovikj will be speaking about Africas ancient disease landscape and Dr Erik Karlsson will talk about metagenomics and high-risk interfaces tinyurl.com/ytj3sppm
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Erik Karlsson @eakarlsson.bsky.social · 25/10/2025
Proud to be part of this new Nature Biotechnology paper, “RNA structure modulates Cas13 activity and enables mismatch detection.” Detecting single-nucleotide mutations in #influenza or SARS-CoV-2 is how you know, fast, when a virus is playing by different rules. www.nature.com/articles/s41...
nature.com
RNA structure modulates Cas13 activity and enables mismatch detection - Nature Biotechnology
An effective CRISPR RNA occlusion strategy enhances mismatch detection when using Cas13.
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Erik Karlsson @eakarlsson.bsky.social · 23/10/2025
Now out in @nejm.org : Between 2023–2024: Sixteen human infections with A/H5N1 in Cambodia. Six deaths. Most in children. All exposed to sick or dead poultry. www.nejm.org/doi/full/10....
nejm.org
Resurgence of Zoonotic Highly Pathogenic Avian Influenza A(H5N1) Virus in Cambodia | NEJM
In this report from Cambodia, 16 human cases of highly pathogenic avian influenza A(H5N1) virus infection that occurred from February 2023 through August 2024 are described.
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Erik Karlsson @eakarlsson.bsky.social · 07/08/2025
Time’s running out! We’re hiring 1 Scientist + 2 Postdocs at @PasteurCambodia’s #Virology Unit to work on emerging viruses & #zoonoses. If you want to do real-time science that matters—this is your chance. Apply now. Start soon. 🦠🔬🧪🐓💉🦇😷🥼 #academicjobs #OneHealth #Virology
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Erik Karlsson @eakarlsson.bsky.social · 06/08/2025
Cambodia has confirmed its 15th human case of #H5N1 in 2025. That brings the year’s total to 15 cases and 7 deaths (CFR: 46.6%). Since 2005: 87 cases, 50 deaths (CFR: 57.5%). 🧪🧬🥼🦠🔬😷🐓💉 #AvianInfluenza #Zoonoses #BirdFlu #Spillover
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Erik Karlsson @eakarlsson.bsky.social · 29/07/2025
Cambodia has confirmed its 14th human case of avian influenza A/H5N1 in 2025 : a 26-year-old man from Siem Reap. So far in 2025: 14 cases, 7 deaths — a case fatality rate (CFR) of 50% Since 2005: 86 cases, 50 deaths (CFR: 58.1%) 🧪🧬🥼🦠🔬😷🐓💉
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Erik Karlsson @eakarlsson.bsky.social · 22/07/2025
13th human case of #H5N1 in Cambodia this year: 6-year-old boy from Tbong Khmum province, confirmed on July 21. Exposure likely linked to sick and dead poultry. He is currently in intensive care. 🧪🧬🥼🦠🔬😷🐓💉
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Erik Karlsson @eakarlsson.bsky.social · 11/07/2025
**JOBS ALERT** The Virology Unit at @PasteurCambodia hiring 1 Scientist and 2 Postdocs to join our fast-moving, field-connected, research-driven team on emerging viruses and zoonoses. 🧪🧬🥼🦠🔬🐓💉🦇😷 Limited time to apply — and we need people to start ASAP.**👇
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Erin Harvey @erinharvey.bsky.social · 05/07/2025
Got a great idea for a metagenomic virus discovery project but not sure what to do next? We are running a 5 day hands on workshop in beautiful Stellenbosch, South Africa with experts from around the world. Applications are open until 31st July. climade.health/2025/06/22/m...
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Erik Karlsson @eakarlsson.bsky.social · 03/07/2025
12th case of H5N1 in Cambodia in 2025. 5 yo boy from Kampot. Zoonotic spillover continues to occur. Vigilant surveillance and One Health response is critical.
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Erik Karlsson @eakarlsson.bsky.social · 02/07/2025
The Virology Unit at IPC is constantly working to make surveillance/Early Warning faster, better, cheaper — from air sampling to portable labs. Happy to have our work featured in this @telegraphnews.bsky.social article by @sneweyy.bsky.social 🦠🧪🐓💉🥼😷 Read more: www.telegraph.co.uk/global-healt...
telegraph.co.uk
From coop to cave: Inside the high-tech hunt for H5N1 and Disease X
The Telegraph joined scientists in Cambodia’s vibrant wet markets and vast bat caves to test revolutionary new disease surveillance tools
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Erik Karlsson @eakarlsson.bsky.social · 01/07/2025
11th case of H5N1 in Cambodia has now been reported. Known exposure to sick poultry. This is the 7th case in June, and the 4th in Siem Reap. Continued vigilance, active surveillance, and a strong One Health response remain critical. #BirdFlu 🦠🔬🧪🐓💉😷🥼
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Erik Karlsson @eakarlsson.bsky.social · 29/06/2025
Cambodia has confirmed its 9th and 10th human cases of H5N1 bird flu this year. 6 of these cases occurred in June alone. Sadly, 6 people have died in 2025. 🧪🧬🦠🔬🥼😷🐓💉
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Erik Karlsson @eakarlsson.bsky.social · 02/04/2025
A long time coming, but our @nanoporetech.com P2Solo is finally running. Time to dive deeper into the messy unknown, hunt down mysterious pathogens, and maybe even find some shiny new viruses. Let's do this. 🦇🐓🧪🦠🧬🔬 #Nanopore #VirusHunting #Science #OneHealth #Genomics
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Erik Karlsson @eakarlsson.bsky.social · 29/03/2025
I echo @systemsvirology.bsky.social - if anyone needs some support or ways to work, please reach out.
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Erik Karlsson @eakarlsson.bsky.social · 23/03/2025
A virus won’t go from “nothing” to “crisis” overnight—but ignoring it is like smelling smoke and thinking, “Eh, probably just toast.” Spoiler: it’s not toast. Early Warning is everything. Fund and improve systems that keep the kitchen from burning down. 🧪🦇🔬🦠💉😷 #ViroSky #IDSky
medscape.com
Experts: New Bat Coronavirus Being Watched
Expert advocates continued vigilance related to recent announcement of newly discovered coronavirus.
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Erik Karlsson @eakarlsson.bsky.social · 23/03/2025
Yet another reminder that A/H5N1 is everywhere: Cambodia’s MoH just confirmed the country’s 75th case. A young child exposed to sick/dead poultry is critically ill. Staying alert, acting fast, and keeping people informed is how we prevent more spillover. 🧪🐓🦠😷💉 #ViroSky #IDSky tinyurl.com/mrxw5xew
https://www.facebook.com/story.php?story_fbid=1075471541276275&id=100064403181076&mibextid=wwXIfr&rdid=K0JvQkOCq6JVaOXE
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Pretzel @krispyhajkowicz.bsky.social · 18/03/2025
Scientists, clinicians and public health from across the Pacific are discussing pathogen genomic surveillance at the Institut Pasteur de Novelle Caledonie at the stunning Pacific Community Building in Noumea. Here, @eakarlsson.bsky.social leads a discussion of wet lab technical requirements.
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Erik Karlsson @eakarlsson.bsky.social · 18/03/2025
We must shift our mindset and upgrade how quickly, accurately, and cheaply we can detect pathogens, even before they become outbreaks. The next pandemic isn't hypothetical; it's guaranteed. Time for more bold innovation and real-world action. #ViroSky #IDSky 🥼🦠🔬🧪🧬
npr.org
How the pandemic changed the world of disease control for worse -- and for better
Five years after the World Health Organization declared a global pandemic, there has been progress — and backsliding in the way the world responds to infectious disease.
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Erik Karlsson @eakarlsson.bsky.social · 14/03/2025
Postdoc Opportunity Got a PhD in disease evolution, or something similarly hardcore? Know your way around phylodynamics? Good. We need you. If you’re up for real-world research getting hands-on with fieldwork, sequencing, and making sense of viral evolution, apply here: jobs.inrae.fr/en/ot-25456.
jobs.inrae.fr
Postdoctoral research project: Phylodynamics of highly pathogenic avian influenza viruses in complex ecosystems H/F
ContextHighly pathogenic avian influenza (HPAI) viruses are rapidly crossing geographical boundaries, threatening poultry, wildlife and potentially evolving into global pandemics1,2. In South-East Asi...
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Erik Karlsson @eakarlsson.bsky.social · 25/02/2025
The Virology Unit at IPC has 3 positions open in #OneHealth: *Postdoc – Reconstructing Past Outbreaks *Postdoc – Environmental Surveillance *Clinical Manager These aren’t just jobs. They’re front-row seats to global health in action. Ready? tinyurl.com/57rvxcau #ViroSky #IDSky 🦠🔬🧬🥼🧪
tinyurl.com
Institut Pasteur du Cambodge on LinkedIn: The Institut Pasteur du Cambodge (IPC) is looking for: -…
The Institut Pasteur du Cambodge (IPC) is looking for: - 𝐏𝐨𝐬𝐭𝐝𝐨𝐜𝐭𝐨𝐫𝐚𝐥 𝐑𝐞𝐬𝐞𝐚𝐫𝐜𝐡𝐞𝐫 – 𝐒𝐞𝐫𝐨𝐥𝐨𝐠𝐲 𝐚𝐭 𝐭𝐡𝐞 𝐇𝐮𝐦𝐚𝐧-𝐀𝐧𝐢𝐦𝐚𝐥…
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Michelle Wille @duckswabber.bsky.social · 21/02/2025
Smart surveillance really coming into its own. Air, water, and surface sampling in bird markets w NGS can outperform traditional swab based approaches in detecting in a diversity of viruses, including avian influenza. Amazing work by @E_A_Karlsson + team 👉 www.researchsquare.com/article/rs-5...
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Erik Karlsson @eakarlsson.bsky.social · 16/02/2025
I know things are rough right now for a lot of people in science, and job hunting isn’t exactly fun—but if you’re a virologist looking for interesting work and want a scenery change, the Virology Unit at Institut Pasteur in Cambodia is hiring. #virosky #idsky tinyurl.com/y62d6tnw
linkedin.com
Erik Karlsson on LinkedIn: Senior Scientist for the Virology Unit
The job market can feel like a bad dating app—lots of vague promises, unrealistic expectations, and the occasional ghosting. You’re out here swiping through…
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Brandon Hayes @brandonhayes.bsky.social · 15/02/2025
Interested in doing a PhD along the lines of transmission dynamics, disease ecology or epidemiology? Check out iddjobs.org — whole bunch of new opportunities posted this past week!
iddjobs.org
IDDjobs
Find infectious disease dynamics modelling jobs, studentships, and fellowships.
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Erik Karlsson @eakarlsson.bsky.social · 13/02/2025
Environmental sampling—air, water, and surfaces—in live bird markets coupled with NGS can outperform traditional poultry swabs in avian influenza (H5N1) and other zoonotic threats. Check out our preprint here: www.researchsquare.com/article/rs-5... #virosky #idsky 🧪🦠🔬🧬🐓
researchsquare.com
Air sampling accurately captures circulating zoonotic viral diversity emerging from poultry live-animal markets
Environmental surveillance has emerged as a pivotal strategy for early detection of pathogens that pose threats to humans (1) but has not been utilized for zoonotic agents. In Asia, live-bird markets ...
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American Society for Virology @amersocvirology.bsky.social · 03/02/2025
Today is the abstract deadline for ASV2025 in Montreal, Canada! Submit by 11:59 pm ET tonight (2/3)! asv.org/asv2025/abst...
asv.org
Abstract Submission | American Society for Virology
Abstract submission for the ASV 2025 annual meeting July 14-17, 2025, in Montreal, Quebec, Canada. Hosted by McGill University.
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Erik Karlsson @eakarlsson.bsky.social · 15/01/2025
Honored to be speaking at the @nationalacademies.org Forum on Microbial Threats workshop on Preventing Patient Zero today. www.nationalacademies.org/event/43921_... #virosky #idsky
nationalacademies.org
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Dr Fifa A Rahman @fifarahman.bsky.social · 15/01/2025
Very cool innovations utilised at Institut Pasteur du Cambodge presented by @eakarlsson.bsky.social - drones and remote control cars to collect environmental samples at locations that are high risk for avian influenza.
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Robert de Vries @rpdevrieslab.bsky.social · 13/01/2025
We have a new preprint on the receptor specificity of 2.3.4.4 H5 viruses. We introduced the hallmark Q226L mutation in several antigenic backgrounds and observed different phenotypes. #H5N1 #glycotime www.biorxiv.org/content/10.1...
biorxiv.org
The Q226L mutation can convert a highly pathogenic H5 2.3.4.4e virus to bind human-type receptors
H5Nx viruses continue to wreak havoc in avian and mammalian species worldwide. The virus distinguishes itself by the ability to replicate to high titers and transmit efficiently in a wide variety of h...
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CIDRAP @cidrap.bsky.social · 10/01/2025
Cambodian man dies from H5N1 avian flu, possibly after eating sick chickens This is the 19th human H5N1 case identified in Cambodia since early 2023. www.cidrap.umn.edu/a... Photo: Paul Korecky / Flickr cc
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Erik Karlsson @eakarlsson.bsky.social · 10/01/2025
Avian influenza #H5N1 continues to cause infections and deaths globally, including in Southeast Asia. Vigilant One Health surveillance and response is critical to detecting and preventing avian flu. 🦠🧪🔬🧬 www.facebook.com/share/p/1PM9...
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Erik Karlsson @eakarlsson.bsky.social · 20/12/2024
Tis the season for #holiday lights. #avianinfluenza sequencing up and running on our new #mk1d from ⁦‪Oxford Nanopore at ⁦‪Pasteur Cambodia‬⁩ . #nanopore #oxfordnanopre #genomic #h5n1 #alliwantforchristmas #anywhereanything #virosky #idsky 🧪🦠🧬🔬🥼🥼🧑‍🔬
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Erik Karlsson @eakarlsson.bsky.social · 13/12/2024
New toys for the holidays. Just got hands on the #Mk1d from #nanopore. Looking forward to using this in the field as we continue to make surveillance better, faster, and cheaper. #avianinfluenza #oxfordnanopore #anywhereanything 🦠🧪🔬🧬
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Erik Karlsson @eakarlsson.bsky.social · 10/12/2024
Happy to be hosting the Pasteur Network Asia-Pacific Avian Influenza Symposium here in Phnom Penh this week organized by Pasteur Cambodia and HKU Pasteur - first time all nine of these institutes have met under this network! #avianinfluenzasymposium #avianflu #pasteurnetwork #ipc
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Michelle Wille @duckswabber.bsky.social · 02/12/2024
Surveillance is hard, laborious, expensive. Even more so in the Antarctic. With @eakarlsson.bsky.social we highlight how to enhance our understanding of HPAI using innovative surveillance approaches. 👉https://www.sciencedirect.com/science/article/pii/S0169534724002787#f0010
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Erik Karlsson @eakarlsson.bsky.social · 29/11/2024
The emergence of HPAI in Antarctica’s vulnerable wildlife merits a rapid response supported by global coordination and scientific innovation due to the potential impact on both fauna and the ecosystem. #ViroSky #IDSky www.sciencedirect.com/science/arti...
sciencedirect.com
A call to innovate Antarctic avian influenza surveillance
Highly pathogenic avian influenza (HPAI) viruses are increasingly spreading between birds and mammals globally, with sporadic transmission to humans. …
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